Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate Ga0059261_1675 Ga0059261_1675 acetylornithine deacetylase (ArgE)
Query= curated2:Q9ABF3 (386 letters) >FitnessBrowser__Korea:Ga0059261_1675 Length = 395 Score = 84.3 bits (207), Expect = 5e-21 Identities = 66/219 (30%), Positives = 105/219 (47%), Gaps = 21/219 (9%) Query: 58 NLYARRGTARPNLCFAGHTDVVPVGDDAAWTAGPFEAEIKEGVLYGRGAVDMKSAIAAFV 117 NL+A G+ + +GH+DVVPV D W + PF E ++G+L+GRG DMK IAA + Sbjct: 62 NLFATIGSGEGGIVLSGHSDVVPV-DGQDWHSNPFVLEERDGLLFGRGTCDMKGFIAACL 120 Query: 118 AAV-----ANVPDHPGSISFLITGDEEGVAEDGTVKVVEALAAEGEIIDHCIVGEPTSAN 172 A V AN+ + + I+ DEE + G ++E L A G C+VGEPTS Sbjct: 121 AKVPMLASANLNE---PVHLAISFDEE-IGCKGAGHMIEELVARGLRPRGCVVGEPTSME 176 Query: 173 LLGDMVKIGRRGSINAWITVEGRQGHVAYPHRAANPVPVLVDILSALKA-----RVLDDG 227 + IG + V G + H + N + +++ ++A R + Sbjct: 177 PV-----IGHKTGSAYGCAVHGLEAHSSLAPYGVNAIFYAARLIARIEAIAARLRAEERR 231 Query: 228 YTGFQ-PSNLEITTIDVGNTATNVIPAAAKARVNIRFNP 265 + G+ P + + G A+N++PA + R +IR P Sbjct: 232 HPGYSVPFSTLSAGVIEGGQASNIVPALCRFRFDIRTLP 270 Lambda K H 0.318 0.135 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 392 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 386 Length of database: 395 Length adjustment: 31 Effective length of query: 355 Effective length of database: 364 Effective search space: 129220 Effective search space used: 129220 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory